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Date of Award
Jared M. Schrader
Gene expression is an essential process of all organisms which occurs in two steps, mRNA transcription, and translation and which is shut off by mRNA decay. For a bacterium to grow and divide, these steps need to be tuned to optimize the synthesis rates of thousands of proteins from their genes. Genome-wide experiments were used to determine the absolute transcription rates, mRNA degradation rates, and translation rates on a gene by gene basis in the model bacterium Caulobacter crescentus. This not only provides a system biology view of the organism’s gene expression resource allocation, but also provides a chance to understand the interconnections between the sub-steps of gene expression. Co-transcriptional mRNA decay was determined to affect nearly a third of mRNAs in the bacterium, which likely has regulatory consequences for these genes. Different strategies for producing mRNA at the correct level were found that either optimize for efficiency or for regulatory control. We observed that there is strong evidence that higher translation efficiency and slows mRNA decay, and that this is likely due to protection provided by ribosomes sterically hindering the RNA degradosome from cutting the mRNA. Finally, absolute translation rates revealed the fitness costs of Vitamin B12 scavenging from the highly expressed Vitamin B12 importer protein and B12 dependent and independent methionine biosynthesis pathways. We found that across Caulobacter species there was a tradeoff where obligate scavengers had higher fitness when growing in a vitamin B12 rich environment, but lower fitness when growing in vitamin B12 deficient environment due to the high cost of protein synthesis.
Aretakis, James Raymond, "Global Coordination Between Gene Expression Processes In C. Crescentus" (2021). Wayne State University Dissertations. 3437.